Mercurial > repos > devteam > sam_to_bam
comparison sam_to_bam.xml @ 12:9bd1568619cd draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 12:31:54 +0000 |
| parents | 1e69848b596f |
| children |
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| 11:1e69848b596f | 12:9bd1568619cd |
|---|---|
| 14 @PREPARE_FASTA_IDX@ | 14 @PREPARE_FASTA_IDX@ |
| 15 | 15 |
| 16 samtools view | 16 samtools view |
| 17 -b | 17 -b |
| 18 -@ \$addthreads | 18 -@ \$addthreads |
| 19 -t '$reffai' | 19 -t "\$reffai" |
| 20 '$input' | | 20 '$input' | |
| 21 | 21 |
| 22 samtools sort | 22 samtools sort |
| 23 -O bam | 23 -O bam |
| 24 -@ \$addthreads -m \$addmemory"M" | 24 -@ \$addthreads -m \$addmemory"M" |
| 65 <param name="addref_select" value="history" /> | 65 <param name="addref_select" value="history" /> |
| 66 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> | 66 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> |
| 67 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> | 67 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> |
| 68 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> | 68 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> |
| 69 </test> | 69 </test> |
| 70 <test> | |
| 71 <!-- Test direct use of bgzipped reference --> | |
| 72 <param name="addref_select" value="history" /> | |
| 73 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" /> | |
| 74 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> | |
| 75 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> | |
| 76 </test> | |
| 77 <test> | |
| 78 <!-- Test with simple gzipped reference, which requires decompression --> | |
| 79 <param name="addref_select" value="history" /> | |
| 80 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" /> | |
| 81 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> | |
| 82 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> | |
| 83 </test> | |
| 70 </tests> | 84 </tests> |
| 71 <help><![CDATA[ | 85 <help><![CDATA[ |
| 72 **What it does** | 86 **What it does** |
| 73 | 87 |
| 74 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands. | 88 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands. |